Various lines of evidence suggest that large portions of hydrothermal systems in the oceanic crust acts like a giant bioreactor that mediates water-rock exchange and buffers the chemical composition of seawater. We review the current literature and present new chemical, biological and petrographic data on microbially mediated alteration of glass in the oceanic crust. Microbial alteration of glass displays characteristic bioalteration features, in particular in the alteration fronts around residual glass in the oceanic crust, suggesting that microbes take on an active role in its dissolution. Such features are found throughout the oceanic crust ranging in age from a few million to 170 Ma and they are found down to crustal depths of 500m, possibly defining a Deep Oceanic Biosphere (DOB) that covers up to 2/3 of the earth’s surface area. Microbial glass alteration substantially increases the active surface area of dissolving glass particles thereby enhancing the reaction rates during microbially aided dissolution. Microbially mediated glass alteration involves the establishment of two types of diffusion barriers including hydration rinds and biofilms that play an important role in mediating glass alteration. In particular biofilms may be very active by creating a localized chemical environment conducive to glass alteration, and by sequestering dissolved chemical inventory from solution. When compared with abiotic alteration of the oceanic crust, bio-alteration causes more rapid deposition of biotic and abiotic reaction products in the oceanic crust that result in a more effective removal of elements from seawater and a more rapid sealing of the oceanic crust. Thus, it is likely that microbial activity increases the fluxes of seawater components into the crust, while reducing the low-temperature flux of basalt components into seawater. However, much about the microbial activity and its relationships to the chemistry of hydrothermal systems still remains to be explored.